| Literature DB >> 34249702 |
Hao Fu1, Weiming Mi2, Boju Pan3, Yucheng Guo4,5, Junjie Li3, Rongyan Xu6, Jie Zheng4,5, Chunli Zou4,5, Tao Zhang2, Zhiyong Liang3, Junzhong Zou1, Hao Zou4,5.
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancer types worldwide, with the lowest 5-year survival rate among all kinds of cancers. Histopathology image analysis is considered a gold standard for PDAC detection and diagnosis. However, the manual diagnosis used in current clinical practice is a tedious and time-consuming task and diagnosis concordance can be low. With the development of digital imaging and machine learning, several scholars have proposed PDAC analysis approaches based on feature extraction methods that rely on field knowledge. However, feature-based classification methods are applicable only to a specific problem and lack versatility, so that the deep-learning method is becoming a vital alternative to feature extraction. This paper proposes the first deep convolutional neural network architecture for classifying and segmenting pancreatic histopathological images on a relatively large WSI dataset. Our automatic patch-level approach achieved 95.3% classification accuracy and the WSI-level approach achieved 100%. Additionally, we visualized the classification and segmentation outcomes of histopathological images to determine which areas of an image are more important for PDAC identification. Experimental results demonstrate that our proposed model can effectively diagnose PDAC using histopathological images, which illustrates the potential of this practical application.Entities:
Keywords: convolutional neural network; deep learning; histology; pancreatic ductal adenocarcinoma (PDAC); whole-slide image analysis
Year: 2021 PMID: 34249702 PMCID: PMC8267174 DOI: 10.3389/fonc.2021.665929
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
Figure 1Framework of the deep-learning approach. (A) Training data with raw WSIs. (B) Annotated WSIs. (C) Patches for training the patch-level segmentation. Each patch has a region with carcinoma. (D) Two classes of patches for training the patch-level classifier. (E) Testing data with raw WSIs. (F) Heatmap, as the output of the patch-level segmentation. (G) Malignant probability heatmap.
Distribution of patches extracted from the raw WSIs for training the patch-level classifier.
| Class | Testing | Training | Validation | Total |
|---|---|---|---|---|
| Normal | 4,988 | 39,900 | 4,988 | 49,876 |
| Carcinoma | 4,960 | 39,688 | 4,964 | 49,612 |
| Total | 9,948 | 79,588 | 9,952 | 99,488 |
Figure 2Results of the patch-level classification for the test data. (A) Confusion matrix for binary patch classification. (B) ROC. (C) Heatmap of cancer probability generated by our trained classifier. (D) Confusion matrix for binary WSI classification.
The 36 features extracted from a heatmap of malignant probabilities at the WSI-level.
| Feature | Description of feature | The number of features |
|---|---|---|
| 1–9 | Mean, variance, standard deviation, median, mode, minimum, maximum, range, sum of normal probabilities | 9 |
| 10–18 | Mean, variance, standard deviation, median, mode, minimum, maximum, range, sum of tumor probabilities | 9 |
| 19–20 |
| 2 |
| 21–22 |
| 2 |
| 23–24 |
| 2 |
| 25–26 |
| 2 |
| 27–28 |
| 2 |
| 29–30 |
| 2 |
| 31–32 |
| 2 |
| 33–34 |
| 2 |
| 35 | Numeric label of the category to which the largest value for the mean of | 1 |
| 36 | Numeric label of the category with the most patches | 1 |
Performance of patch-level classification.
| Class | Accuracy | Precision | Recall | F1-score |
|---|---|---|---|---|
| Normal | 0.9533 | 0.9728 | 0.9330 | 0.9525 |
| Cancerous | 0.9353 | 0.9738 | 0.9542 |
Performance of patch-level segmentation.
| Training | Validation | Test | Total | |
|---|---|---|---|---|
| 1,385 | 184 | 163 | 1732 | |
| Average dice | – | 0.7602 | 0.8465 | – |
Figure 3Results of patch-level segmentation. (A) A sample raw patch. (B) Annotated patch. (C) Mask generated by the annotation. (D) Heatmap of the sample patch predicted by our method. (E) A sample WSI with annotation. (F) Heatmap of the sample WSI comprising the heatmaps predicted for each patch.
Figure 4Visualizations of different pancreatic lesions by Grad-CAM and the corresponding heatmaps. (A–D) Positive sets with cancerous tissues. (E, F) Negative sets with background or normal tissue. The four columns from left to right are patch extracted from WSIs, mask generated from the annotation, Grad-CAM and heatmap presentation for these patches, respectively.
Figure 5Independent verification results. (A) Sample WSI labeled as carcinoma by TCGA. (B) Cancer probability heatmap from our WSI classification method.